I use the cheap MF towels on my windows too, and I had terrible linting problems shortly after I first got them. I have since washed my MF towels several times, and this has dramatically reduced the linting.
If you already have lint on your windows, you can partially remove it with clean MF towels. When you press the MF towel against the glass and swipe it, some of the lint will be picked up by the towel, and some will be pushed accross the surface of the window. I start and end my windshield swipes at the A-pillar, and I have noticed that I have much more lint by the pillar than I have in the middle of the windshield.
Therefore, you can sweep the existing lint on the middle of your windshield to the side. Then you can swipe the MF towel down the side, and, if you remove your hand quickly and smoothly enough, you will remove a lot of lint. I use a combination rolling and lifting motion. With my hand flat against the windshield, I start with my fingers. I roll them up toward my face until my wrist locks. At this point, only the heel of my palm is against the glass. I then smoothly lift up the heel of my palm. This method picks up a lot of MF lint.